FAIR Research Objects and Computational Workflows – A Linked Data Approach

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https://w3id.org/ro/doi/10.5281/zenodo.8113625

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FAIR Research Objects and Computational Workflows – A Linked Data Approach
description
RO-Crate of PhD thesis at the University of Amsterdam
datePublished
2024-07-30
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temporalCoverage
2019-06/2024-05
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graad van doctor
sourceOrganization
dateModified
2024-11-15
identifier
url
https://s11.no/2023/phd/
cite-as
https://doi.org/10.5281/zenodo.8113625
isAccessibleForFree
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Haris Antonatos

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#haris-antonatos

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Haris Antonatos
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SciFY, Athens, Greece

Supplemental material

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#supplements

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(23 / 23)

Supplement 1: Ten Simple Rules for making a software tool workflow-ready

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https://s11.no/2022/phd/10-simple-rules-for-workflow-tools/

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Supplement 1: Ten Simple Rules for making a software tool workflow-ready
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Paul Brack, et al. (2022): Ten Simple Rules for making a software tool workflow-ready. PLOS Computational Biology 18(3):e1009823

Supplement 2: Enhancing RDM in Galaxy by integrating RO-Crate

ScholarlyArticle

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https://s11.no/2022/phd/galaxy-ro-crate/

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Supplement 2: Enhancing RDM in Galaxy by integrating RO-Crate
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Paul De Geest, et al. (2022): Enhancing RDM in Galaxy by integrating RO-Crate. Research Ideas and Outcomes 8:e95164

Supplement 3: Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory

ScholarlyArticle

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https://s11.no/2021/phd/workflow-collaboratory/

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Supplement 3: Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory
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Carole Goble, et al. (2021): Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory. Zenodo (white paper)

Supplement 4: Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language

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https://s11.no/2022/phd/methods-included/

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Supplement 4: Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language
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Michael R. Crusoe, et al. (2022): Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language. Communications of the ACM 65(6)

Supplement 5: Semantic micro-contributions with decentralized nanopublication services

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https://s11.no/2021/phd/nanopub/

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Supplement 5: Semantic micro-contributions with decentralized nanopublication services
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Tobias Kuhn, et al. (2021): Semantic micro-contributions with decentralized nanopublication services. PeerJ Computer Science 7:e387

Supplement 6: Perspectives on automated composition of workflows in the life sciences

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https://doi.org/10.12688/f1000research.54159.1

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Supplement 6: Perspectives on automated composition of workflows in the life sciences
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Anna-Lena Lamprecht, et al. (2021): Perspectives on automated composition of workflows in the life sciences. F1000Research 10:897

Supplement 7: ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data

ScholarlyArticle

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https://doi.org/10.1007/978-3-030-80960-7_16

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Supplement 7: ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data
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Rudolf Wittner, et al. (2023): ISO 23494: Biotechnology – Provenance Information Model for Biological Specimen And Data. Lecture Notes in Computer Science 12839
url
https://research.manchester.ac.uk/en/publications/2de95545-9fd6-4a51-91ee-dad30058afe5

Supplement 8: Towards a Common Standard for Data and Specimen Provenance in Life Sciences

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https://doi.org/10.1002/lrh2.10365

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Supplement 8: Towards a Common Standard for Data and Specimen Provenance in Life Sciences
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Rudolf Wittner, et al. (2023): Toward a common standard for data and specimen provenance in life sciences. Learning Health Systems 8(1):e10365

Supplement 9: A Community Roadmap for Scientific Workflows Research and Development

ScholarlyArticle

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https://doi.org/10.1109/WORKS54523.2021.00016

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Supplement 9: A Community Roadmap for Scientific Workflows Research and Development
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Rafael Ferreira da Silva, et al. (2021): A Community Roadmap for Scientific Workflows Research and Development. 2021 IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS).
url
https://doi.org/10.48550/arXiv.2110.02168

Supplement 10: Unique, Persistent, Resolvable: Identifiers as the Foundation of FAIR

ScholarlyArticle

Identifier

https://doi.org/10.1162/dint_a_00025

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Supplement 10: Unique, Persistent, Resolvable: Identifiers as the Foundation of FAIR
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Nick Juty, et al. (2020): Unique, Persistent, Resolvable: Identifiers as the Foundation of FAIR. Data Intelligence 2(1-2)

Supplement 11: FAIR Computational Workflows

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https://doi.org/10.1162/dint_a_00033

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Supplement 11: FAIR Computational Workflows
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Carole Goble, et al. (2020): FAIR Computational Workflows. Data Intelligence 2(1-2)

Supplement 12: Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv

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Identifier

https://doi.org/10.1093/gigascience/giz095

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Supplement 12: Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv
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Farah Zaib Khan, et al. (2019): Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv. GigaScience 8(11)

Supplement 13: IEEE Standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication: IEEE Std 2791-2020

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https://doi.org/10.1109/ieeestd.2020.9094416

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Supplement 13: IEEE Standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication: IEEE Std 2791-2020
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url
https://research.manchester.ac.uk/en/publications/936de52b-ac53-4f0e-9927-77fd7073e88d

Supplement 14: BioHackEU22 Project 22: Plant data exchange and standard interoperability

ScholarlyArticle

Identifier

https://doi.org/10.37044/osf.io/c724r

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Supplement 14: BioHackEU22 Project 22: Plant data exchange and standard interoperability
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Daniel Arend, et al. (2022): BioHackEU22 Project 22: Plant data exchange and standard interoperability. BioHackrXiv

Supplement 15: RO-Crate, a lightweight approach to Research Object data packaging

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https://s11.no/2019/phd/ro-crate/

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Supplement 15: RO-Crate, a lightweight approach to Research Object data packaging
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Eoghan Ó Carragáin, et al. (2019): RO-Crate: A lightweight approach to research object data packaging. RO-15 at Workshop on Research Objects (RO 2019), IEEE eScience 2019, 2019-09-24, San Diego, CA, USA.

Supplement 16: Federated causal inference based on real-world observational data sources: application to a SARS-CoV-2 vaccine effectiveness assessment

ScholarlyArticle

Identifier

https://s11.no/2023/phd/federated-causal-inference/

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Supplement 16: Federated causal inference based on real-world observational data sources: application to a SARS-CoV-2 vaccine effectiveness assessment
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Marjan Meurisse, et al. (2023): Federated causal inference based on real-world observational data sources: Application to a SARS-CoV-2 vaccine effectiveness assessment. BMC Medical Research Methodology 23:248

Supplement 17: Linking provenance and its metadata in multi-organizational environments of life sciences

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Identifier

https://s11.no/2023/phd/linking-provenance/

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Supplement 17: Linking provenance and its metadata in multi-organizational environments of life sciences
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Rudolf Wittner, et al. (2023): Linking provenance and its metadata in multi-organizational environments of life sciences.

Supplement 18: BioHackEU22 Report: Enhancing Research Data Management in Galaxy and Data Stewardship Wizard by utilising RO-Crates

ScholarlyArticle

Identifier

https://s11.no/2023/phd/enhancing-rdm-galaxy-dsw/

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Supplement 18: BioHackEU22 Report: Enhancing Research Data Management in Galaxy and Data Stewardship Wizard by utilising RO-Crates
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Ignacio Eguinoa, et al. (2023): BioHackEU22 Report: Enhancing Research Data Management in Galaxy and Data Stewardship Wizard by utilising RO-Crates. BioHackrXiv

Supplement 19: BioHackEU23 report: Enabling continuous RDM using Annotated Research Contexts with RO-Crate profiles for ISA

ScholarlyArticle

Identifier

https://doi.org/10.37044/osf.io/7y2jh

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Supplement 19: BioHackEU23 report: Enabling continuous RDM using Annotated Research Contexts with RO-Crate profiles for ISA
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Sebastian Beier, et al. (2024): BioHackEU23 report: Enabling continuous RDM using Annotated Research Contexts with RO-Crate profiles for ISA. BioHackrXiv

Supplement 20: BioHackEU23 report: Enabling FAIR Digital Objects with RO-Crate, Signposting and Bioschemas

ScholarlyArticle

Identifier

https://s11.no/2024/enabling-fair-digital-objects/

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Supplement 20: BioHackEU23 report: Enabling FAIR Digital Objects with RO-Crate, Signposting and Bioschemas
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Stian Soiland-Reyes, et al. (2024): BioHackEU23 report: Enabling FAIR Digital Objects with RO-Crate, Signposting and Bioschemas. BioHackrXiv

Supplement 21: Report on "FAIR Signposting" and its uptake by the community

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https://s11.no/2024/signposting-report/

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Supplement 21: Report on "FAIR Signposting" and its uptake by the community
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Mark D Wilkinson, et al. (2024): Report on FAIR Signposting and its Uptake by the Community. EOSC FAIR Metrics and Data Quality Task Force

Supplement 22: Practical webby FDOs with RO-Crate and FAIR Signposting: Experiences and lessons learned

ScholarlyArticle

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https://s11.no/2024/webby-fdos/

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Supplement 22: Practical webby FDOs with RO-Crate and FAIR Signposting: Experiences and lessons learned
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Stian Soiland-Reyes, et al. (2024): Practical webby FDOs with RO-Crate and FAIR Signposting: Experiences and lessons learned. International FAIR Digital Objects Implementation Summit 2024, Berlin, Germany, 2024-03-20/--21. Open Conference Proceedings 4 (submitted)

Stian Soiland-Reyes

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https://orcid.org/0000-0001-9842-9718

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Stian Soiland-Reyes
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Department of Computer Science, The University of Manchester, Manchester, UK
Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands
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Peter Sefton

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https://orcid.org/0000-0002-3545-944X

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Peter Sefton
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School of Languages and Cultures, The University of Queensland, Brisbane, Queensland, Australia
Faculty of Science, University Technology Sydney, Australia (former)
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Simone Leo

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https://orcid.org/0000-0001-8271-5429

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Simone Leo
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Center for Advanced Studies, Research, and Development in Sardinia (CRS4), Pula (CA), Italy
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Leyla Jael Castro

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https://orcid.org/0000-0003-3986-0510

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Leyla Jael Castro
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ZB MED Information Centre for Life Sciences, Cologne, Germany
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Claus Weiland

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https://orcid.org/0000-0003-0351-6523

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Claus Weiland
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Herbert Van de Sompel

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Herbert Van de Sompel
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The University of Manchester

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The University of Manchester
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University of Amsterdam

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University of Amsterdam
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Packaging research artefacts with RO-Crate

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https://doi.org/10.3233/DS-210053

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Packaging research artefacts with RO-Crate
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Mercè Crosas

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https://orcid.org/0000-0003-1304-1939

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Mercè Crosas
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Barcelona Supercomputing Center, Barcelona, ES
Secretària de Govern Obert, Catalunya, Barcelona, ES (former)
Institute for Quantitative Social Science, Harvard University, Cambridge, MA, USA (former)

José Mª Fernández

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https://orcid.org/0000-0002-4806-5140

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José Mª Fernández
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Barcelona Supercomputing Center, Barcelona, Spain
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Daniel Garijo

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https://orcid.org/0000-0003-0454-7145

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Daniel Garijo
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Ontology Engineering Group, Universidad Politécnica de Madrid, Madrid, Spain
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Björn Grüning

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https://orcid.org/0000-0002-3079-6586

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Björn Grüning
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Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany

Marco La Rosa

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Marco La Rosa
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PARADISEC, Melbourne, Australia
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Eoghan Ó Carragáin

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https://orcid.org/0000-0001-8131-2150

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Eoghan Ó Carragáin
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University College Cork, Ireland
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Marc Portier

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https://orcid.org/0000-0002-9648-6484

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Marc Portier
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Vlaams Instituut voor de Zee (VLIZ), Oostende, Belgium
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Ana Trisovic

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https://orcid.org/0000-0003-1991-0533

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Ana Trisovic
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Institute for Quantitative Social Science, Harvard University, Cambridge, MA, USA
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RO-Crate Community

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https://www.researchobject.org/ro-crate/community

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RO-Crate Community
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2024-07-30T15:20:00Z
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Paul Groth

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https://orcid.org/0000-0003-0183-6910

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Paul Groth
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Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands
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Carole Goble

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https://orcid.org/0000-0003-1219-2137

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Carole Goble
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affiliation
Department of Computer Science, The University of Manchester, Manchester, UK
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Packaging research artefacts with RO-Crate (RO-Crate)

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https://w3id.org/ro/doi/10.5281/zenodo.5146227

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name
Packaging research artefacts with RO-Crate (RO-Crate)
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Oscar Corcho

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https://orcid.org/0000-0002-9260-0753

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Oscar Corcho
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Raul Palma

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https://orcid.org/0000-0003-4289-4922

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Raul Palma
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Frederik Coppens

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https://orcid.org/0000-0001-6565-5145

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Frederik Coppens
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affiliation
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
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Kyle Chard

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https://orcid.org/0000-0002-7370-4805

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Kyle Chard
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Jose Manuel Gomez-Perez

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https://orcid.org/0000-0002-5491-6431

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Jose Manuel Gomez-Perez
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Michael R. Crusoe

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https://orcid.org/0000-0002-2961-9670

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Michael R. Crusoe
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affiliation
Forschungszentrum Jülich, Jülich, Germany
Department of Computer Science, VU Amsterdam, Amsterdam, The Netherlands
Common Workflow Language project, Software Freedom Conservancy, Brooklyn, NY, USA
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Ignacio Eguinoa

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https://orcid.org/0000-0002-6190-122X

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Ignacio Eguinoa
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affiliation
Showpad, Ghent, Belgium
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium (former)
VIB-UGent Center for Plant Systems Biology, Ghent, Belgium (former)
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Nick Juty

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Identifier

https://orcid.org/0000-0002-2036-8350

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Nick Juty
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Kristi Holmes

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https://orcid.org/0000-0001-8420-5254

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Kristi Holmes
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Jason A. Clark

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https://orcid.org/0000-0002-3588-6257

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Jason A. Clark
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Salvador Capella-Gutierrez

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https://orcid.org/0000-0002-0309-604X

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name
Salvador Capella-Gutierrez
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affiliation
Life Sciences Department. Barcelona Supercomputing Center (BSC), Barcelona, Spain
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Alasdair J. G. Gray

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https://orcid.org/0000-0002-5711-4872

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Alasdair J. G. Gray
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Stuart Owen

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https://orcid.org/0000-0003-2130-0865

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name
Stuart Owen
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affiliation
Department of Computer Science, The University of Manchester, Manchester, UK
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Alan R Williams

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https://orcid.org/0000-0003-3156-2105

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name
Alan R Williams
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affiliation
Department of Computer Science, The University of Manchester, Manchester, UK (former)
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Giacomo Tartari

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https://orcid.org/0000-0003-1130-2154

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Giacomo Tartari
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Finn Bacall

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https://orcid.org/0000-0002-0048-3300

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Finn Bacall
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Department of Computer Science, The University of Manchester, Manchester, UK
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Thomas Thelen

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https://orcid.org/0000-0002-1756-2128

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Thomas Thelen
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Hervé Ménager

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https://orcid.org/0000-0002-7552-1009

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name
Hervé Ménager
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affiliation
Hub de Bioinformatique et Biostatistique, Département Biologie Computationnelle, Institut Pasteur, Paris, France
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Laura Rodríguez-Navas

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https://orcid.org/0000-0003-4929-1219

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name
Laura Rodríguez-Navas
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affiliation
Universitat Oberta de Catalunya (UOC), Barcelona, Spain
Life Sciences Department. Barcelona Supercomputing Center (BSC), Barcelona, Spain (former)
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Paul Walk

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https://orcid.org/0000-0003-1541-5631

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Paul Walk
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brandon whitehead

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https://orcid.org/0000-0002-0337-8610

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brandon whitehead
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Mark Wilkinson

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https://orcid.org/0000-0001-6960-357X

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Mark Wilkinson
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Erich Bremer

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Identifier

https://orcid.org/0000-0003-0223-1059

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Erich Bremer
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Karl Sebby

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https://orcid.org/0000-0001-6022-9825

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Karl Sebby
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Alexander Kanitz

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https://orcid.org/0000-0002-3468-0652

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name
Alexander Kanitz
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affiliation
Biozentrum, University of Basel, Basel, Switzerland
Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Gavin Kennedy

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https://orcid.org/0000-0003-3910-0474

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Gavin Kennedy
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Mark Graves

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https://orcid.org/0000-0003-3486-8193

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Mark Graves
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Jasper Koehorst

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https://orcid.org/0000-0001-8172-8981

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Jasper Koehorst
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Paul Brack

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https://orcid.org/0000-0002-5432-2748

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name
Paul Brack
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affiliation
Department of Computer Science, The University of Manchester, Manchester, UK (former)
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Milan Ojsteršek

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https://orcid.org/0000-0003-1743-8300

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Milan Ojsteršek
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Bert Droesbeke

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https://orcid.org/0000-0003-0522-5674

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name
Bert Droesbeke
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affiliation
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
VIB Center for Plant Systems Biology, Ghent, Belgium
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Chenxu Niu

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https://orcid.org/0000-0002-2142-1731

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Chenxu Niu
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Kosuke Tanabe

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https://orcid.org/0000-0002-9986-7223

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Kosuke Tanabe
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Tomasz Miksa

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https://orcid.org/0000-0002-4929-7875

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Tomasz Miksa
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Cedric Decruw

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https://orcid.org/0000-0001-6387-5988

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Cedric Decruw
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Andreas Czerniak

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Identifier

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Oliver Woolland

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Beatriz Serrano-Solano
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Bioinformatics Group, Albert-Ludwigs-University Freiburg, Freiburg, Germany

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Laurence Livermore
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The Natural History Museum, London, UK

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Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain

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Genís Bayarri
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Institute for Research in Biomedicine (IRB Barcelona), The Barcelona
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Vrije Universiteit Amsterdam, Amsterdam, The Netherlands

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Ania Niewielska
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European Bioinformatics Institute (EMBL-EBI), Cambridge, UK

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Bogdan Gavrilović
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Pau Andrio
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The Spanish National Bioinformatics Institute (INB), Barcelona Supercomputing Center (BSC), Barcelona, Spain

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Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Shizuoka, Japan
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Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden

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Institute of Data Science, Maastricht University, Maastricht, The Netherlands

s11

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s11
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Appendix A: Acknowledgement

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https://s11.no/2022/phd/acknowledgements/

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Appendix A: Acknowledgement
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Section 5.1: Making Canonical Workflow Building Blocks interoperable across workflow languages

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https://s11.no/2022/phd/canonical-workflow-building-blocks/

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Section 5.1: Making Canonical Workflow Building Blocks interoperable across workflow languages
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Stian Soiland-Reyes, et al.(2022): Making Canonical Workflow Building Blocks interoperable across workflow languages. Data Intelligence 4(2)

Chapter 6: Discussion and conclusions

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Section 6.2: Conclusion

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Appendix B: Contributions

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Section 4.2: Creating lightweight FAIR Digital Objects with RO-Crate

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https://s11.no/2022/phd/fdo-with-ro-crate/

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Section 4.2: Creating lightweight FAIR Digital Objects with RO-Crate
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Stian Soiland-Reyes, et al. (2022): Creating lightweight FAIR Digital Objects with RO-Crate. Research Ideas and Outcomes 8:e93937

Section 5.3: Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows

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https://s11.no/2022/phd/incrementally-building-fdos/

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Section 5.3: Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows
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Oliver Woolland, et al. (2022): Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows. Research Ideas and Outcomes 8:e94349

Chapter 1: Introduction

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https://s11.no/2022/phd/introduction/

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Research Question 1, aims for FAIR Digital Objects on the Web
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text
Can the promising FDO concept be realised using existing Web technology, taking into account the lessons learnt from the early Semantic Web developments and more recent Linked Data practices?

RQ2

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https://s11.no/2022/phd/introduction/#rq2

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RQ2
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Research Question 2, aims for FAIR Research Objects
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text
Can a more pragmatic use of Linked Data practices better implement Research Objects for a wider developer audience, by using familiar Web technologies and give lightweight recommendations?

RQ3

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https://s11.no/2022/phd/introduction/#rq3

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Research Question 3, ims for FAIR Computational Workflows
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Can a FAIR Digital Object approach for computational workflows unify machine-readable descriptions of Research Software, data and provenance, which can be consistently implemented by developers of different workflow management systems?

Section 4.1: Packaging research artefacts with RO-Crate

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https://s11.no/2022/phd/ro-crate/

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Section 4.1: Packaging research artefacts with RO-Crate
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Stian Soiland-Reyes, et al. (2022): Packaging research artefacts with RO-Crate. Data Science 5(2)

Section 4.3: Formalizing RO-Crate in First Order Logic

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https://s11.no/2022/phd/ro-crate/formalizing/

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Section 4.3: Formalizing RO-Crate in First Order Logic
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Section 5.2: The Specimen Data Refinery: A canonical workflow framework and FAIR Digital Object approach to speeding up digital mobilisation of natural history collections

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https://s11.no/2022/phd/specimen-data-refinery/

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Section 5.2: The Specimen Data Refinery: A canonical workflow framework and FAIR Digital Object approach to speeding up digital mobilisation of natural history collections
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Alex Hardisty, et al. (2022): The Specimen Data Refinery: A canonical workflow framework and FAIR Digital Object approach to speeding up digital mobilisation of natural history collections. Data Intelligence 4(2)

Section 3.2: Updating Linked Data practices for FAIR Digital Object principles

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https://s11.no/2022/phd/updating-ld-for-fdo/

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Section 3.2: Updating Linked Data practices for FAIR Digital Object principles
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Stian Soiland-Reyes, et al. (2022): Updating Linked Data practices for FAIR Digital Object principles. Research Ideas and Outcomes 8:e94501

Chapter 2: Background

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https://s11.no/2023/phd/background/

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Chapter 2: Background
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In this chapter, we discuss the related work with respect to FAIR Digital Objects and Linked Data. We do so by looking through the lens of development of these technologies over time, including future directions.
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Section 3.1: Evaluating FAIR Digital Object and Linked Data as distributed object systems

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https://s11.no/2023/phd/evaluating-fdo/

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Section 3.1: Evaluating FAIR Digital Object and Linked Data as distributed object systems
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Stian Soiland-Reyes, et al. (2024): Evaluating FAIR Digital Object and Linked Data as distributed object systems. PeerJ Computer Science 10:e1781
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https://doi.org/10.7717/peerj-cs.1781

Comparison tables for Evaluating FAIR Digital Object and Linked Data (RO-Crate)

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Chapter 3: FAIR Digital Objects and Linked Data

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https://s11.no/2023/phd/fdo-and-linked-data/

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Chapter 3: FAIR Digital Objects and Linked Data
description
To investigate RQ1 this chapter evaluates both Linked Data and FAIR Digital Object (FDO) as ways to realize the FAIR principles. Section 3.1 compares the two approaches as global distributed object systems, and discusses what lessons can be learnt across the communities, taking into consideration the history covered by section 2. Section 3.2 proposes how the FDO principles can be achieved using Linked Data standards, which is explored further in the following chapters.
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References

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https://s11.no/2023/phd/references/

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References

Chapter 4: RO-Crate

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https://s11.no/2023/phd/ro-crate/

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Chapter 4: RO-Crate
description
This chapter introduces RO-Crate, a pragmatic method of packaging data alongside structured metadata that is inline with the FAIR principles. This has been implemented to investigate RQ2. Section 4.1 describes the RO-Crate purpose, community effort and tooling and demonstrates how RO-Crate has been applied. Section 4.2 shows how RO-Crate can be used to achieve the FDO principles covered in chapter 3. Section 4.3 contributes a formal definition of RO-Crate using first order logic.
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Section 5.4: Recording provenance of workflow runs with RO-Crate

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https://s11.no/2023/phd/workflow-run-crate/

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Section 5.4: Recording provenance of workflow runs with RO-Crate
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Simone Leo, et al. (2024): Recording provenance of workflow runs with RO-Crate. PLoS ONE 19(9):e0309210

Recording provenance of workflow runs with RO-Crate (RO-Crate and mapping)

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https://w3id.org/ro/doi/10.5281/zenodo.10368989

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Chapter 5: Computational Workflows

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Identifier

https://s11.no/2023/phd/workflows/

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Chapter 5: Computational Workflows
description
In order to investigate RQ3, and considering important parts of the FAIR principles are Reuse and provenance, this chapter examines in closer details how FAIR Digital Objects and RO-Crate can be used with Computational Workflows. Section 5.1 proposes that tools in computational workflows, when wrapped as interoperable building blocks, can be considered as FAIR Digital Objects, with a use case from biomolecular simulation. Sections 5.2 and 5.3 explore how FDOs and Research Objects can be constructed incrementally using computational workflows, with a use case from specimen digitization in natural history collections. Section 5.4 presents a profile of RO-Crate to capture workflow execution provenance, with incremental granularity levels and six workflow engine implementations. Use cases include machine learning-aided tumour detection and compatibility with PROV approaches.
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FAIR Research Objects and Computational Workflows – A Linked Data Approach

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https://s11.no/2023/phd/thesis.pdf

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FAIR Research Objects and Computational Workflows – A Linked Data Approach
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2024-09-15
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https://zenodo.org/records/14052581/files/phd-stian-2024-11-07.pdf
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Cover art for book cover of thesis, created with several public domain cliparts
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ro-crate-metadata.json

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